A Very Advanced Ark
by fanficoholic
Summary: What if the Doctor wasn't as alone as he thought?
1. Interlude

"My love, I need you to be safe."

"Mum?"

"The War is coming and I know that something bad is going to happen."

"But..."

"I'm going to send you away from Gallifrey," she told him, kissing his forehead, "To a planet called Earth. The Doctor has claimed the planet under his protection and you know how much the other's hate dealing with him."

"But he's..."

"He'll keep you safe my love," she told him, "Especially considering that you're his son."

The Time Lady gave her son one last hug before pulling down the heavily modified chameleon arch and placing it on the young Gallifreyan's head.

"You're taking my memories?" The child exclaimed.

His mother shook her head, "The only way for you to be safe is if you're considered just another human. This arch will transform you, but I've fixed it so that you can keep impressions of your memories. Human bodies cannot cope with Time Lord brains."

"But I..." He began to scream. His mother held him firmly in her arms as the chameleon arch changed her son's DNA. She soothed him the best she could, desperate for forgiveness. No mother ever wanted to put their child in so much pain. Finally it was over, and she only felt one heart beating. She gently removed the device from his head and slowly removed her son's Time Lord essence: it made a handsome fob watch. Laying him down on the ground, using her balled up jacket for a pillow, she made the young potential Time Lord to be comfortable. Once she was sure that he was situated, she turned her attention to the central station.

"Avery Ada," she said gently. A semi-corporeal presence suddenly appeared. "I need you to do me a favor."

Avery Ada looked down on her mistress, friend, and companion's son, "Anything," she replied, "You only need to ask."

"The last, greatest and most terrible Time War is on the horizon. It is quite obvious, to me at least, that there will be no victory. The Daleks came to do one thing, and one thing only; to exterminate the Time Lords and I do not wish that fate to befall my only child."

Avery Ada hummed, "I understand," she said, "I take it you need me to keep your child safe."

"He is human," she told the beautiful ship, "And until he is ready to fend for himself, I need you to watch over him."

"Is he to be my new companion?"

She rested her hand gently on the console, "There is no one I trust more," she said.

Avery Ada bowed, "It is my honor, Time Lord."

As they hurtled through time and space towards Earth, she sat on the ground, her son's head cradled in her lap. She gently stroked his head, memorizing as much of him as she could. When they finally arrived, she gently kissed his brow and whispered something in his ear before standing up and carrying him outside her ship. Avery Ada used this opportunity to transform herself into a more corporeal form, transforming from ship to a young teenaged humanoid shape. She gently accepted the young boy into her arms.

"Keep him safe," she whispered, a tear crawling down her cheek.

Avery Ada nodded, "I will protect him with my life."

She handed the fob watch to Avery Ada, "You'll know when he's ready," she said. She then pulled something out of her pocket and clasped it around his wrist. Kissing his brow once more before backing away from the boy and his ship, she stared at them for the longest time and after gently touching her pendant, she disappeared. That would be the last time Avery Ada ever saw her mistress, friend and companion, Preyala, the Artisan.


	2. Chapter 1

It took little time to establish them as brother and sister, and to find a family that would raise the young potential Time Lord as their own. She explained that they had survived a most horrific event and that her brother need a home and a family. An older couple, Ioan and Betrys Jones took the child in without hesitation. Since Avery refused to give them his name they decided to call him Ifan Dafydd. When he woke up, he knew nothing. His memories of the past were buried deep in his subconscious, protecting him from the emotional trauma of knowing that his mother all but abandoned him on a different planet to keep him safe from death.

Between his loving parents and his doting yet protective older sister, Ifan, or as he liked to be called Ianto, adapted to his new life like a duck to water. He was well aware that he was adopted by the older couple but he didn't care, they were his parents and he loved them almost as much as they him. Avery had a harder time adapting, but over time she became more and more human-like. She never shied from her duty, but over time she began to live as few of her kind ever had.

When Ianto turned eighteen, he decided that it was time to stand on his own two feet. The urge to travel ran strong in him, so he spent an entire year traveling the world, unsuspecting that his sister was never too far behind. His mother died first, of stomach cancer, and soon after his Tad died too, officially of a heart attack, but both Avery and Ianto knew that he couldn't live without his beloved wife. At age 20, Ianto decided to settle for a bit in London to go to school. He studied many subjects, taking full advantage of the system, not really settling on one mere topic. His mind absorbed information like a sponge, gaining the attention of Torchwood whose director decided to hire him within days of their meeting.

By day he was a student, soaking in every scrap of knowledge that he could, by night he worked for Torchwood as a junior Archivist, learning everything about the universe and beyond. Avery didn't like Torchwood, especially after learning that the Doctor was their enemy, but knew that she really had no true say. All she could do was protect him and ensure that he keep an open mind about the last know Time Lord in existence.

When Canary Wharf happened, Avery almost revealed herself to her young master. She had an ingrained hatred of all things Dalek and knew that without a doubt, that if they knew who Ianto truly was, they'd kill him in a heartbeat. She wanted to spirit him off to safety, but luckily the Doctor managed to find his way to the center of the battle and defeated the enemy, allowing Ianto to keep his life, in more ways than one.

"Thank Pythia that you are safe," Avery exclaimed the moment she spotted him. She engulfed him in her arms, relieved that he was still breathing. If a Gallifreyan died while under the effects of the Chameleon Arch, that death would most likely be permanent.

Normally Ianto would try and wiggle out of her arms, deeming himself too old to be coddled, but at that moment he little cared. He needed to feel safe. The duo closed themselves in Avery's London apartment for a month, Ianto recovering from the trauma that was battle, and Avery just basking in his continued presence.

He changed from the young man that Avery knew. He was quieter for one, taking time to absorb the situation before any action was taken on his behalf. And from time to time he disappeared for a few hours, not letting Avery know where he went. She decided that he needed space so didn't pester him. She figured that if he needed her help, he would ask for it. Finally Ianto announced his intentions to move back to Cardiff.

"We can leave inside a month," Avery told him, "Just give me time to make a few arrangements."

Ianto gave her a sad smile, "Actually I was hoping to be on my own for a while."

Avery blinked, obviously confused, "I don't understand."

He sighed, "I think its time for me to really be on my own. You've been there for me all my life, its time you do something for yourself. I love you, Avery, but you really need to get a life."

Avery didn't know what to say. How did one explain to another that their entire existence was devoted to their well-being? She knew Ianto wasn't ready yet. He was still too young to know about his true origins and yet he was rightfully too old to have a babysitter so to speak. Finally she just sighed and accepted his decision. He needed space and while his sister couldn't join him, she might be able to pull off mimicking a lamppost of something similar to keep an eye on him.

It took Ianto only a week to prepare his return to Cardiff. Apparently his apartment had already been put on the market: he had wanted to buy a bigger place with his late girlfriend,Lisa. Avery drove him to the train station, and waved him off. She had already sold her own apartment and was ready to go incognito for how ever long it took Ianto to miss her. After moving to an empty alley, she closed her eyes and for the first time in over a decade, transformed her outer form. Within a few moments she had managed to apparate, she had read a few Harry Potter books and liked the term, to Cardiff and disguise herself as a lamp post right outside his apartment. Of course she put a light perception filter up so no one would question her absence when she moved, but all in all it was the perfect hiding spot, that was until she realized that Ianto wouldn't be staying in his flat much.

She huffed and decided that an alternate strategy would have to be devised. Back in her human form, but with a full on perception filter, Avery followed her brother, wondering just where the Gallifreyan spent his days. She caught him standing inside of a Tourist Office with a thermos. She was confused until a man in a long blue coat came out and began talking to Ianto. Avery scanned the man, never having seen him before, and identified him as Captain Jack Harkness. History was full of mentions of the man. Apparently he had been around since the eighteen hundreds on Earth. She moved closer and frowned. There was something strange about Harkness, and it wasn't the fact that he exhibited traits only found in 51st century humans. She moved even closer before she realized just what felt off about the man. He was a fixed point in time!

Avery couldn't believe what her sensors were telling her. Events were fixed in time, not people! It was impossible, a fundamental law of time said so. She ran through different scenarios, trying to figure out how it could have happened when she realized that Ianto had given her the slip. She was torn between figuring out the impossibility of Jack Harkness and her sworn duty to protect Ianto. Finally she decided to try again another day, knowing that her duty lied with Ianto before anything.

Over the next week Ianto brought coffee for the impossibility. She wondered if it was a bizarre new mating ritual. But just before she could establish herself on the Plass, he did something different. It was night and Ianto was standing in the middle of a street, waiting for something. A few minutes later, Harkness showed up. They squabbled for a bit before Jack tried to walk away and Ianto said something about a pterodactyl.

The next morning, Ianto was back on the plass, but this time instead of staying in the Tourist Office, he was invited even further inside. She planted herself on top of the water tower, perception filter at full blast. Between her station as a lamp post and her station on top of the water tower, she was ready to keep an eye on Ianto. It didn't hurt that being on the Plass invigorated her.

Ianto called Avery every few days, updating her on his status. He told her about his new job as a civil servant, and how he basically took care of his group. He complained about someone named Owen, was tight lipped about his boss, Jack, and praised their computer technician, Toshiko. There was another girl, Suzie, but Ianto didn't really like her much. Avery was glad that she had integrated her cellphone into her systems. It made keeping up appearances much easier.

A few months later, Ianto needed her. He had a full month off of work and seemed very stressed and depressed. She ached to be close to him, to give the young man she considered her brother some comfort but couldn't really do anything unless he called her. When he finally did call, she insisted that she come visit and that was that. It was hard waiting the appropriate amount of time allowed for a train ride, but she just barely managed. The moment Ianto opened the door for her, she engulfed him in an embrace and steered him to his bed. He broke down, crying.

"What happened Dai?" She asked.

"She's gone," he whimpered, "Lisa..."

Avery didn't question why it took him so long to react to his late girlfriend's death. Instead she just held him close, and reminded him that he was never alone. Finally she managed to pull a story out of him about how Lisa had been in a coma since Canary Wharf and how he had to turn off her life support. Avery knew that there was more to it than that, but didn't push. He'd tell her when he could. He also told her about how he was using company resources to help Lisa, betraying Jack and the rest of the team, how he had been suspended and how much it hurt to see the betrayal on their faces.

"They'll forgive you Dai," she told him.

"How?"

Avery gave him a smile, "Because you did what you did for love. They'll be mad at you for a while, feel betrayed, but in the end they'd understand because they would have probably done the same in your position."

When Ianto returned to work, things got worse before they got better. He managed to earn his team's forgiveness in time, and told Avery about how he was getting closer to his boss. By the year's end, Ianto fully admitted to sleeping with his boss. He had grown to care about Jack, letting Avery know that the impossibility would become a part of their lives.

Avery was sitting on the water tower, minding her own business when she spotted a blue police box materialize out of nowhere. She immediately recognized the Tardis and quickly turned off anything that could give her away. She spotted the Doctor but before she could even consider meeting him and his Tardis, he was ready to depart once more, but not before Jack ran up to the Tardis and latched unto the side. Avery got much more vigilant. Not only did she suspect that Ianto would need to talk soon, but it was also clear that Jack knew about Time Lords.

The year that never was was probably the worst year Avery had ever experienced, and she was thousands of years old. Between the poor Tardis being transformed into a Paradox Machine by the Master, Ianto risking his neck forming a resistance, and having to hide lest be picked up by the Master, she needed a long break. When she sensed the Angel Network broadcast the thoughts of practically all the humans on Earth, Avery knew she had to act. As a Gallifreyan, Ianto was very sensitive to time and when it reset, the closer he was to the singularity event, the more likely he would remember when everyone else did not. She had to get him as far away from Cardiff as she could. Luckily she was close enough to him that she could grab the young potential Time Lord and teleport him to China. She then returned to Cardiff and watched as time reset itself. When the calendar was reset, she checked on Ianto and was relieved that he had no memories from before the reset.

Over time Avery realized that Ianto was a member of Torchwood once more. She was rather annoyed with her brother, but what could she do? It wasn't like she could walk up to him and tell him that he couldn't work for Torchwood. She wasn't even supposed to know about the crown-sanctioned group.


	3. Chapter 2

Avery was sitting on the Water Tower, soaking up the Rift energy when all of a sudden there was an explosion. She almost fell off the tower. She immediately set her scanners on the hub, scanning for life signs when she spotted Ianto fighting to get out from under the rubble. Not caring about the consequences, she apparated to him.  
>"Ianto!" She cried out, "Are you hurt?"<br>"Avery?"  
>Avery just started moving the rubble so that she could get access to Ianto. When he was finally free, she engulfed him in one of her signature hugs.<br>"Never again!" She told him, "You hear me? You are never working for Torchwood ever again. This is the second time you almost died in a Torchwood building and I am not allowing for a third."  
>"Avery, what?"<br>"No time to explain Ianto," she said, "You're not safe here."  
>She pulled him behind her, making sure to expand her perception filter, and led him to a dark alley. Ianto was about to speak when Avery used the Tardis' example and transformed into a red Police Phone box. His eyes widened in disbelief.<br>"Ianto get inside!" Avery ordered and without a moment's hesitation, Ianto obeyed. He had been conditioned over the years to obey his sister when she barked commands at him.  
>"What? How?"<br>Avery used her non-corporeal form, "Have a seat and don't touch anything. We need to get you to safety."  
>She immediately set the coordinates for the moon, 100 years into the future. As far as she could tell, they would be safe there. She also sent out a beacon, summoning the Doctor.<br>"What the bloody hell is going on?" Ianto demanded.  
>Avery walked over to Ianto and sat down besides him, "You're not human, Ianto." She began, "You're a Time Lord."<br>"I'm a what?"  
>Avery closed her eyes and suddenly Ianto's fob watch was hovering between them, "Open it," she told him.<br>Ianto shook his head, "Not until I know what's happening."  
>Avery sighed, "Please..."<br>Ianto shook his head, refusing.  
>"Ianto Dafydd Jones, open the damned fob watch. Not only will you get your answers but it will save time as well."<br>Ianto hesitated, "Will it hurt me?" He asked in a small voice.  
>Avery sighed, "Yes," she said honestly, "But the good outweighs the bad. Please Ianto, would I ever make you do something like this if it wasn't necessary?"<br>Ianto looked at whom he assumed to be his sister. He felt betrayed and angry with her for so many reasons, but at the same time he still trusted her. She never led him astray and had been there for him as long as he could remember. Finally he just opened the watch and waves of agony embraced him. Everything rushed at him, his memories, knowledge and most importantly the essence of whom he truly was. While the physical pain ended, the emotional pain was just as excruciating.  
>"Mother?"<br>Avery Ada blinked rapidly, "She's..." She cleared her throat, "Everyone is gone, well everyone save for you and the Doctor."  
>"It hurts," he whimpered.<br>"Focus on me little one," she said, "Block everything else out. Focus on me, on this single point in time and space. You're not alone, not as long as you have me."  
>It took a while, but finally, Ianto managed to focus solely on Avery. He remembered everything, and knew what had happened. He was alone in the universe. Ianto had never felt so big nor so small.<br>"Ianto I..."  
>Suddenly Avery Ada froze and then her non-corporeal form disappeared. Ianto called for her and she sent him a soothing reassurance through their mental link. He finally took the chance to look around. Everything was suddenly so much bigger. He tried to stand up, but struggled. He looked down and his clothes were swimming on him. He panicked for a moment, before Avery sent him a soothing sensation. Taking a deep calming breath, Ianto struggled out of his suit jacket, his dress shirt, trousers, and shoes, leaving him in his white undershirt. He folded everything, and set it in the corner before making his way to the center of the room, and huddling as close to the console as he could, needing to be close to what was considered Avery Ada's soul. Everything started shaking until finally it stopped. Avery Ada reappeared and asked Ianto to step outside.<br>"Avery?"  
>"Please," she whispered, gently caressing his mind.<br>Ianto took a deep breath before stepping outside of his ship. He stumbled slightly, needing to adjust his center of gravity, but made it without falling. The moment he exited, Avery Ada resumed her humanoid form and wrapped her arms around him in a hug. He was relieved, not wanting to be alone.  
>"Ave?" He asked quietly, "What happened?"<br>Avery stood up, taking Ianto with her. The young Time Lord looked to be ten years old again. As a human, at his age, he was an adult, but in Time Lord years meant that he was barely into his preteens. She cuddled him closely, savoring the feel of him in her arms once more.  
>"You're a Time lord again, Dai," she said, "And Time Lords age differently to humans. When the Chameleon Arch turned you back, it turned you into who you're supposed to be, age and all."<br>"But I was an adult," Ianto said, "I had sex and everything..."  
>Avery couldn't help but grimace, "Please don't say that," she asked, "You're a child now. As a human, you aged...matured by their standards. Now that you're back to your original form, you'll find that you're no where near ready to be on your own let alone in any sort of relationship. Ianto Jones was a disguise, and while there are elements of his personality in you"<br>"But why am I ten?"  
>Avery took a moment to plot her answer, "Time lord children take about 100 human years to mature into what human's look like at age 18. So when you looked six, thirty human years passed. Do you understand?"<br>Ianto frowned, "I think so," he said, "So even though I've lived 24 human years..."  
>"Actually you've lived 54 human years," Avery interrupted, "On Galliffrey, our years are longer."<br>Ianto groaned, "My head hurts," he said.  
>Avery grinned, "Don't worry little brother," she said, "You'll get it eventually."<br>Ianto finally looked around and spotted the Earth in the distance, "Ave? Where are we?"  
>"We're on the moon," she told him, "About fifty years into the future."<br>"And why are we fifty years into the future on the moon?"  
>"We're waiting for someone," she said simply.<br>"For who?"  
>"Whom," Avery corrected, and suddenly there was a strange sound, "And here they are."<br>Ianto watched as a blue 1950s Police Box appeared in front of them. His eyes widened, "Is that who I think it is?"  
>Avery didn't reply. Instead they watched as the police box doors opened, revealing a man in a brown trench coat, a suit and converse. Ianto cringed at the fashion faux pas but had to admit that it worked for the man.<br>"Its been a long time Doctor," Avery said, putting Ianto down.  
>"Blimey," he whispered, "Avery Ada, is that really you?"<br>"In the flesh," she said, accepting his embrace, "So to speak."  
>"Where have you been? Is Preya..."<br>Avery Ada shook her head sadly, "I'm sorry Doctor, but Preya is gone."  
>The Doctor frowned sadly before wiping away that expression and pulling on a more curious face, "Well then, who's this?"<br>Avery Ada beamed, pulling Ianto closer, "Doctor, I'd like you to meet Ianto. Dai, this is the Doctor. He's your father."  
>"What?" The Doctor exclaimed, eyes wide.<br>"What?" Ianto asked, his expression identical to the Doctor's.  
>Avery rolled her eyes at the father and son duo, "Oh don't give me that," she said, "What did you think would happen after sleeping with his mother? You know Time lady's are extremely fertile."<br>Ianto grimaced, "I did not need to hear that Ave," he muttered.  
>"And you," she said, looking at Ianto, "Your mother told you about Theta before."<br>Ianto pouted, he was still quite young, "Well excuse me for not remembering. Mum never called him the Doctor, besides, its not like I just got my memories returned by the Chameleon arch." His sarcasm wasn't much affected by his deaging.  
>The Doctor frowned, "The Chameleon arch?" He asked, "Why did you go and use that?"<br>Avery couldn't help but roll her eyes, "How else do you think he survived the Time War?"  
>"But the ramifications of using it on a young mind..."<br>"Preya made some modifications," Avery said, "There were risks, but she managed to mitigate them. Besides, this was the only way that Preya thought of to keep Ianto away from the council."  
>The Doctor winced, "Were they upset about our coupling?" He asked.<br>Avery shrugged, "I don't think they even knew that Ianto was yours."  
>"Ah," The Doctor was torn between relief and disappointment.<br>"Excuse me," said Ianto, "What's going to happen now?"  
>The Doctor cheered up, "Well thats easy," he said, "I'm going to take you with me. Teach you everything I know and then some. You are my son after all."<br>"But I have responsibilities," Ianto protested, "I can't just go off skipping through time and space."  
>"Ianto," Avery said, "Even if we did take you back, what good would you do? You're a child, you look no where near the age you were as a human. Do you think that Jack and Gwen would allow a child to help them right now?"<br>"But I could explain..."  
>"I'm sorry son," said the Doctor, "As much as it pains me to say, you can't reveal yourself to them." Ianto looked almost completely destroyed, making the doctor add, "At least not now."<br>"What?"  
>"Doctor!" Avery hissed.<br>The Doctor ignored the more advanced TARDIS, "When you look the right age, I promise to take you back to this time. It's supposed to happen anyway, you being here is a fixed event."  
>Ianto leapt at the Doctor, grabbing him into a bear hug. He had a wide grin and kept thanking his newly found father over and over again. Avery wasn't happy about the Doctor's promise, but conceded the point. Ianto Jones had been apart of the Day of Regrets. She just hoped that he didn't really die.<br>"How long until I can get back?" Ianto demanded.  
>The Doctor thought about it for a moment, "Around 135 or so Earth years, give or take. But they won't even notice."<br>Ianto winced at the amount of time it would take to get back to what he considered his true age, but conceded defeat. He knew that they were right to prevent him from going to Jack right now. It hurt, but he could do it.  
>"I just need to know one thing," Ianto said, turning his eyes on his sister and father, "Did Jack survive? Being blown up that is."<br>The Doctor winced at the thought of being blown up, "He's a fixed point," he said, "Most likely he can survive anything."  
>Ianto felt his heart breaking, "I need to know!"<br>The Doctor frowned, "You're not supposed to cross your own timeline," he said, "The consequences could be fatal."  
>"Tad, please!" He begged, "I promise I won't do anything to disturb the timeline! I just can't stand spending over a century wondering if Jack made it. I love him!"<br>"You love who?" He asked, "Not Jack Harkness!"  
>Ianto gave the Doctor a look, "Who else?"<br>"But he's wrong!"  
>Ianto's expression darkened, "Jack may be many things, but he is not wrong."<br>The Doctor backpedaled, "I didn't mean it like that!" He exclaimed, "He's not supposed to exist. Humans aren't supposed to be fixed points. Besides, you're too young..."  
>"If Jack wasn't supposed to exist, he wouldn't." Said Ianto simply, "And I may be young but I've lived long enough to know whether or not I truly love someone. You forget that as a human, I was an adult."<br>"Yes well..."  
>"Well come on then!" said Ianto, "It's not like we don't have the time."<p> 


End file.
